Protein secondary structures include 13-sheets/13-turns, 7r-helices, 310-helices, and a-helices.
The a-helix is the most common element of protein secondary structure and participates widely in fundamental biological processes, including highly specific protein-protein and protein-nucleic acids interactions. Molecules that can predictably and specifically disrupt these interactions would be invaluable as tools in molecular biology, and, potentially, as leads in drug development (Kelso et al., J. Am. Chem. Soc. 126:4828-4842 (2004); Schafineister et al., J. Am. Chem. Soc., 122:5891-5892 (2000); Austin et al., J. Am. Chem. Soc. 119:6461-6472 (1997); Phelan et al., J. Am. Chem. Soc. 119:455-460 (1997); Osapay et al., J. Am. Chem. Soc. 114:6966-6973 (1992); Kemp et al., J. Org. Chem. 56:6672-6682 (1991); Jackson et al., J. Am. Chem. Soc. 113:9391-9392 (1991); Ghadiri et al., J. Am. Chem. Soc. 112:1630-1632 (1990); Felix et al., Int. J. Pept. Protein Res. 32:441-454 (1988)). Exposed a-helices on the surfaces of proteins are also often involved in recognition of other biomolecules. Peptides composed of less than fifteen residues corresponding to these a-helical regions typically do not remain helical once excised from the protein environment. Short peptides (<15 residues) that can adopt α-helical structure are expected to be useful models for the design of bioactive molecules and for studying aspects of protein folding.
Several strategies have been reported for the preparation of stabilized α-helices (Andrews et al., “Forming Stable Helical Peptides Using Natural and Artificial Amino Acids,” Tetrahedron 55:11711-11743 (1999)). These methods include incorporation of normatural amino acids (Lyu et al., “Alpha-helix Stabilization by Natural and Unnatural Amino Acids with Alkyl Side Chains,” Proc. Nat'l Acad. Sci. 88:5317-5320 (1991); Kaul et al., “Stereochemical Control of Peptide Folding,” Bioorg. Med. Chem. 7:105-117 (1999)), capping motifs (Austin et al., “Template for Stabilization of a Peptide Alpha-helix: Synthesis and Evaluation of Conformational Effects by Circular Dichroism and NMR,” J. Am. Chem. Soc. 119:6461-6472 (1997); Lyu et al., “Capping Interactions in Isolated Alpha Helices: Position-dependent Substitution Effects and Structure of a Serine-capped Peptide Helix,” Biochemistry 32:421-425 (1993); Chakrabartty et al., “Helix Capping Propensities in Peptides Parallel Those in Proteins,” Proc. Nat'l Acad. Sci. U.S.A. 90:11332-11336 (1993); Kemp et al., “Studies of N-Terminal Templates for Alpha-helix Formation—Synthesis and Conformational-analysis of (2s,5s,8s,11s)-1-acetyl-1,4-diaza-3-keto-5-carboxy-10-thiatricyclo[2.8.1.0(4,8)]tridecane (Ac-Hel1-Oh),” J. Org. Chem. 56:6683-6697 (1991)), salt-bridges (Bierzynski et al., “A Salt Bridge Stabilizes the Helix Formed by Isolated C-Peptide of RNase A,” Proc. Nat'l Acad. Sci. U.S.A. 79:2470-2474 (1982)), metal ion chelation (Kelso et al., J. Am. Chem. Soc., 126:4828-4842 (2004); Kelso et al., “A Cyclic Metallopeptide Induces Alpha Helicity in Short Peptide Fragments of Thermolysin,” Angew. Chem. Int. Ed. Engl. 42:421-424 (2003); Ruan et al., “Metal-ion Enhanced Helicity in Synthetic Peptides Containing Unnatural, Metal-ligating Residues,” J. Am. Chem. Soc. 112:9403-9404 (1990); Ghadiri, J. Am. Chem. Soc., 112:1630-1632 (1990)), and covalent side chain linkers such as disulfide (Jackson et al., “A General Approach to the Synthesis of Short Alpha-helical Peptides,” J. Am. Chem. Soc. 113:9391-9392 (1991)), lactam (Phelan et al., “A General Method for Constraining Short Peptides to an Alpha-helical Conformation,” J. Am. Chem. Soc. 119:455-460 (1997); Bracken et al., J. Am. Chem. Soc. 116:6431-6432 (1994); Osapay et al., J. Am. Chem. Soc., 114:6966-6973 (1992); Felix et al., Int. J. Pept. Protein Res. 32:441-454 (1988)), and hydrocarbon bridges (Schafineister et al., “An All-hydrocarbon Cross-linking System for Enhancing the Helicity and Metabolic Stability of Peptides,” J. Am. Chem. Soc. 122:5891-5892 (2000); Blackwell et al., “Highly Efficient Synthesis of Covalently Cross-linked Peptide Helices by Ring-closing Metathesis,” Angew. Chem. Int. Ed. Engl. 37:3281-3284 (1998)). Stabilization of the α-helix structure with these strategies is typically context dependent (Geistlinger et al., “An Inhibitor of the Interaction of Thyroid Hormone Receptor Beta and Glucocorticoid Interacting Protein,” J. Am. Chem. Soc. 123:1525-1526 (2001); McNamara et al., “Peptides Constrained by an Aliphatic Linkage between Two C(alpha) Sites: Design, Synthesis, and Unexpected Conformational Properties of an i, (i+4)-Linked Peptide,” Org. Chem. 66:4585-4594 (2001)). More importantly, however, these strategies typically block solvent-exposed surfaces of the target α-helices, or restrict or replace important side chain functionalities from the putative α-helices.
Thus, there remains a need for identifying a general method for the synthesis of highly stable internally-constrained peptide structures, such as short α-helical peptides, with strict preservation of the helix surfaces. The present invention is directed to overcoming these and other deficiencies in the art.